Hi. I am a newbie in RNA-Seq analysis and now I am doing the pipeline with several software. I want to use cufflinks ,cuffcompare and cuffdiff to get DE genes,alternative splicing and novel transcripts and now I am confused about the output files cuffdiff gave me and I don't know what to do next. so the queston is:
1 Attached is a image I made to try to figure out the relationship of each file
I got from cuffdiff. But I don't know if it's right. so any advice will be
appreciated
2 If I'm going to analysis the DE,should I get the gene list and do subsequent
analysis like GO enrichment?
If I'm going to analysis alternative splicing difference between the samples.
How should I proceed? statistics the number of AS events, make a
histogram or something?
If I'm going to analysis the novel transcripts ,what am I supposed to do?
Thank you in advance for your advice.
Huijuan
1 Attached is a image I made to try to figure out the relationship of each file
I got from cuffdiff. But I don't know if it's right. so any advice will be
appreciated
2 If I'm going to analysis the DE,should I get the gene list and do subsequent
analysis like GO enrichment?
If I'm going to analysis alternative splicing difference between the samples.
How should I proceed? statistics the number of AS events, make a
histogram or something?
If I'm going to analysis the novel transcripts ,what am I supposed to do?
Thank you in advance for your advice.
Huijuan
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